DNA Repair & the Timeless/Tipin Complex

Science Daily features an article entitled 'Scientists Discover Cellular 'SOS' Signal In Response To UV Skin Damage' which describes a regulatory mechanism which can slow the rate of DNA replication in order to allow for more time to repair DNA damaged by ultraviolet radiation. Regulation is attributed to two proteins known as Timeless and Tipin. The following quote is from the linked article:

"New research from the University of North Carolina at Chapel Hill School of Medicine has identified two proteins that may help protect against skin cancer.

The study, which appears in the advance online edition of the journal Molecular and Cellular Biology, indicates that two proteins, named Timeless and Tipin, form a complex that regulates the rate at which DNA is replicated after exposure to ultraviolet radiation.

Ultraviolet radiation in sunlight damages the DNA in skin cells. If left unrepaired by the cell, this damage can turn into mutations that lead to cancer. Before cells divide, they must replicate, or copy, their DNA to form new daughter cells.

If damage in the DNA is discovered even after the cell has given a "go-ahead" to replicate its DNA, the Timeless/Tipin complex sends a signal throughout the nucleus of the cell to slow the rate of replication. This slowdown may give the cell additional time to repair its DNA and potentially save itself from becoming cancerous or from dying in response to ultraviolet radiation."

DNA repair mechanisms are not limited to "toolkit" responses. In this case a regulatory function, involving the timing of replication, helps maintain genomic integrity.

Responding to Reduced CoA Levels

This from 'Metabolic Strategy Of Stressed Cell': at Biology-blog.com

"The scientists studied the response to decreased CoA in a mouse model by blocking CoA production with hopantenate (HoPan). HoPan is a chemical that interferes with pantothenate kinase (PanK), the enzyme that triggers the first step of CoA production. Following the shutdown of CoA production, the cells quickly recycled CoA from other jobs so it could concentrate all its efforts on a single task: extracting life-supporting energy from nutrients in the mitochondria. Mitochondria are the powerhouses of the cell, so-called because these bags of enzymes host a series of complex biochemical pathways that produce the energy-rich molecule ATPthe cell's "currency" with which it "buys" chemical reactions that consume energy.

"The cell's response to reduced CoA levels is like the driver of a car that is low on gas," said Charles Rock, Ph.D., a member of the St. Jude Infectious Diseases department and co-author of the paper. "The driver might try to save what little gas is left by turning off the air conditioner and driving slower," he said. "Likewise, by shutting down or limiting the other biochemical pathways that use CoA, the cell can concentrate it in the mitochondria where it's needed most."

"The metabolic changes we observed freed up the CoA to make ATP," said Suzanne Jackowski, Ph.D., a member of the St. Jude Infectious Diseases department and the paper's senior author. "Our study provides the first detailed look at how the cell shifts genetic gears to respond to a significant change in its ability to carry on its daily metabolic chores."

A cellular response that would be assumed to have resulted from genetic mistakes that make it through intricate DNA repair mechanisms and become fixed throughout a species as a result of enhanced fitness. We know the drill. An orderly, purposeful process also is consistent with intelligent design. So what standard dictates the choice of paradigms? Evidence that the above actually evolved from a system without a biochemical pathway brake? Or just knowing that it had to?

Around the Blogosphere 3/29/07

http://telicthoughts.com/macneill-is-religion-adaptive/#more-1451

Cornell lecturer Allen MacNeill announces a summer course entitled Evolution and Religion: Is Religion Adaptive?

http://realphysics.blogspot.com/2007/03/discovering-purpose-in-world.html

A reminder from Lawrence Gage that purpose pervades the universe.

http://mindfulhack.blogspot.com/2007/03/non-materialist-neuroscience-watch-new.html

Neuroimaging studies and implications for materialism.

http://mindfulhack.blogspot.com/2007/03/theories-of-everything-theory-of.html

From this blog entry: "Physicists believe that the theory of everything is hovering right around the corner, and yet consciousness is still largely a mystery, and physicists have no idea how to explain its existence from physical laws."

http://www.uncommondescent.com/evolution/the-evolution-of-the-long-necked-giraffe-a-preview/

A new look at the sufficiency of evolutionary explanations for the giraffe's neck.

http://www.uncommondescent.com/intelligent-design/more-reasons-paleoanthropology-has-a-bad-reputation-and-id-continues-its-advance/

Did Leakey manipulate his apelike “Skull 1470” to give it a more human appearence?

http://www.uncommondescent.com/intelligent-design/freeman-dyson-comments-on-id/

Intelligent design is compatible with science according to Freeman Dyson

http://www.newcreationism.org/2007/03/cells-use-noise-to-make-cell-fate.html

Harnessing stochastic fluctuations to drive gene circuits.

New DNA Repair Protein Data

'The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families' appears in PLOS Biology. I believe it to be an extremely fruitful project and am reproducing a part of the linked report in this blog entry. My comments are in bold print. From the paper:

"Proteins Involved in the Repair of UV-Induced DNA Damage

Much of the attention in studies of the microbes in the world's oceans has justifiably focused on phototrophy, such as that carried out by the proteorhodopsin proteins. Previously, in the Sargasso Sea study [10] it was shown that shotgun sequencing reveals a much greater diversity of proteorhodopsin-like proteins than was previously known from cloning and PCR studies. However, along with the potential benefits of phototrophy come many risks, such as the damage caused to cells by exposure to solar irradiation, especially the UV wavelengths. Organisms deal with the potential damage from UV irradiation in several ways, including protection (e.g., UV absorption), tolerance, and repair [78]. Our examination of the protein family clusters reveals that the GOS data provides an order of magnitude increase in the diversity (in both numbers and types) of homologs of proteins known to be involved in pathways specifically for repairing UV damage.

One aspect of the diversity of UV repair genes is seen in the overrepresentation of photolyase homologs in the GOS data (see Table 10). Photolyases are enzymes that chemically reverse the UV-generated inappropriate covalent bonds in cyclobutane pyrimidine dimers and 6–4 photoproducts [79]. The massive numbers of homologs of these proteins in the GOS data (11,569 GOS proteins in four clusters; see Table 10) is likely a reflection of their presence in diverse species and the existence of novel functions in this family. New repair functions could include repair of other forms of UV dimers (e.g., involving altered bases), use of novel wavelengths of light to provide the energy for repair, repair of RNA, or repair in different sequence contexts. In addition, some of these proteins may be involved in regulating circadian rhythms, as seen for photolyase homologs in various species. Our findings are consistent with the recent results of a comparative metagenomic survey of microbes from different depths that found an overabundance of photolyase-like proteins at the surface [51].

A good deal was known about the functions and diversity of photolyases prior to this project. However, much less is known about other UV damage–specific repair enzymes, and examination of the GOS data reveals a remarkable diversity of each of these. For example, prior to this project, there were only some 25 homologs of UV dimer endonucleases (UVDEs) available [80], and most of these were from the Bacillus species. There are 420 homologs of UVDE (cluster 6239) in the GOS data representing many new subfamilies (Figure 7A and Materials and Methods). A similar pattern is seen for spore lyases (which repair a UV lesion specific to spores [81]) and the pyrimidine dimer endonuclease (DenV, which was originally identified in T4 phage [82]). We believe this will also be true for UV dimer glycosylases [83], but predictions of function for homologs of these genes are difficult since they are in a large superfamily of glycosylases.

Our analysis of the kingdom classification assignments suggests that the diversity of UV-specific repair pathways is seen for all types of organisms in the GOS samples. This apparently extends even to the viral world (e.g., 51 of the UVDE homologs are assigned putatively to viruses), suggesting that UV damage repair may be a critical function that phages provide for themselves and their hosts in ocean surface environments. Based on the sheer numbers of genes, their sequence diversity, and the diversity of types of organisms in which they are apparently found, we conclude that many novel UV damage–repair processes remain to be discovered in organisms from the ocean surface water."1

"New repair functions" that might "include repair of other forms of UV dimeers, use of novel wavelengths of light to provide the energy for repair, repair of RNA, or repair in different sequence contexts"- this alone would be a great achievement. But there is more- big increases in the number repair enzymes homologs as well as increased diversity and diversity in UV specific repair pathways extending to the viral world. Suspected new DNA repair processes awaiting discovery and more. Impressive.


References

1. Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families; Shibu Yooseph, Granger Sutton, Douglas B. Rusch1, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachimiak, Christopher van Belle, John-Marc Chandonia, David A. Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J. Raphael, Vineet Bafna, Robert Friedman1, Steven E. Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan S. Taylor, Robert L. Strausberg, Marvin Frazier, J. Craig Venter; PLOS Biology; http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016

What Happens When the Conclusion is Assumed

'Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families' is an article appearing in PLOS Biology and can be viewed at the linked site. Snippets are included in this post for the purpose of commentary. The first of two:

"The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature."1

This sounds like an exciting project likely to yield a gold mine of new data. A vast number of hitherto unknown proteins are being discovered. This includes new protein families and new sequences. But how did this shed light on evolution? Envisioned is the possibility of future inclusions of data within an evolutionary theoretical framework but what are the authors able to state now to back the claim that proteins "shed light on their evolution?" What would have happened if IDists, upon discovering new protein familes, announced that these discoveries had shed light on the intelligent design of such proteins? Can you imagine the reaction? The shedding of light comment makes sense only when an evolutionary outcome is presumed. But if that is the case the discovery can hardly be evidence for the conclusion that evolutionary pathways led to the proteins. More from the cited article:

"Our analysis predicted more than six million proteins in the GOS data—nearly twice the number of proteins present in current databases. These predictions add tremendous diversity to known protein families and cover nearly all known prokaryotic protein families. Some of the predicted proteins had no similarity to any currently known proteins and therefore represent new families. A higher than expected fraction of these novel families is predicted to be of viral origin. We also found that several protein domains that were previously thought to be kingdom specific have GOS examples in other kingdoms. Our analysis opens the door for a multitude of follow-up protein family analyses and indicates that we are a long way from sampling all the protein families that exist in nature."2

An acknowledgement that we are a long way from knowing what remains to be known about all the protein families that exist in nature is reason for pause. Might we be in for surprises that do not accord with current theories and make their revision necessary? Let's wait and see.


References

1. Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families; Shibu Yooseph, Granger Sutton, Douglas B. Rusch1, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachimiak, Christopher van Belle, John-Marc Chandonia, David A. Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J. Raphael, Vineet Bafna, Robert Friedman1, Steven E. Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan S. Taylor, Robert L. Strausberg, Marvin Frazier, J. Craig Venter; PLOS Biology; http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016

2. Ibid

Forgetting an Historic Analytical Process

It is not uncommon to witness the question "Is x designed?" in exchanges with IDists. X can represent a particular organism or, more likely, a biological structure or function of an organism. The answer to the design question is yes but the unasked "What generated the design?" is the more important question. The following is taken from a comment of mine at Telic Thoughts:

Design is evident. Prior to Darwin a natural source was not widely touted because natural selection was not a well known concept. Design was recognized by all and when natural forces were seen as an insufficient explanation rational minds gravitated toward a purposeful, intelligent cause. The Darwinian designer is a natural selection process. Imputing design by IDers entails greater flexibility. The immedate cause may or may not be a process. Purpose may or may not be conflated with underlying natural forces alone. Leaving questions open has the advantage of not closing doors to the implications of future data.

It appears that many of those involved in discussions of intelligent design overlook the fact that standard biological explanations are contingent on the adaquacy of a natural selection explanation. Where evidence of selection is problematic so too are the mainstream arguments linked to it. Many arguments arrayed against intelligent design stand or fall based on the strength of their selection component. For those having difficulty seeing where evidence for intelligent design could come from, take another look at the natural selection paradigm.

Discovering a New Leopard Species

The linked article 'New species declared: Clouded leopard on Borneo and Sumatra' shows that new species are still being found. This one is prominent- a clouded leopard species found on Borneo and Sumatra. As the article states:

"The new clouded leopard species is generally darker than the mainland species, has small cloud markings, many distinct spots within the cloud markings, grayer fur, and a double dorsal stripe. Clouded leopards from the mainland have large clouds on their skin with fewer, often faint, spots within the cloud markings, and they are lighter in color, with a tendency toward tawny-colored fur and a partial double dorsal stripe."

This leopard is Borneo's top predator and is said to have the longest canine teeth, in proportion to its body size, of any cat. The existence of Sumatran tigers on Sumatra means that the leopard is the second largest predator there.

A Birthday

Adolf Butenandt was born in Germany on March 24, 1903 and died on January 18, 1995. He won the Nobel Prize in chemistry in 1939. The following linked item indicates his accomplishments:

"In 1929 he isolated oestrone in pure, crystalline form, almost at the same time that E.A. Doisy did this in America. In 1931 he isolated androsterone in pure, crystalline form. From androsterone he as well as Ruzicka, independently of each other, obtained testosterone in 1939, a compound which had been obtained from the testes in 1935 by Ernst Laqueur. Progesterone was isolated by Butenandt from the corpus luteum in 1934."

Coping with Deamination

Deamination involves the removal of an amine group from a molecule. Maintaining the integrity of DNA can involve subtle strategies. When cytosine is deaminated uracil is the end result. Uracil is found in RNA but its DNA counterpart is thymine. The effect of this is to facilitate mismatch repair.

Before a repair mechanism is set in motion there must be a means of recognizing a mistake. That is much easier to do when the presence of uracil itself is an indicator. Uracil cannot be an indicator in RNA because it is a base unit needed to store and transmit genetic information i.e. it has a legitimate function that would be eliminated along with any uracil resulting from deamination.

An effect of deamination is to disrupt normal base pairing. Since cytosine is paired with guanine a change of cytosine to uracil would also involve a change in base pairing; uracil and thymine being paired with adenine. A change in templates can cause changes in the amino acid content of proteins. The simple substitution of thymine for uracil eliminates many problems.

Allowable Thoughts

Deconstructing Darwinese: Delighting in Ignorance contains commentary on views expressed by science writer Ben Shaberman in the April 2007 issue of Sky and Telescope. Shaberman's piece contains the usual disavowel of intelligent design as an explanation for the universe itself; or perhaps the multiple universes existing in Shaberman's mind. The bottom line: this universe of ours worked out just right as far as conditions favorable to life are concerned. It came down to luck. That's where anti-IDers are willing to go, if necessary, to avoid an intelligent design explanation. The commentary of the Creation Safaris writer is a lot of fun. So let's examine it.

"Darwinese is more than just a language foreign to the majority of people who live by common sense and know an intelligent cause when they see it. No, Darwinese is a complete communication system that includes a set of protocols. One requirement is the secret handshake. This is the motion of sweeping away creationism with a wipe of the hand, and putting “intelligent design” in scare quotes. In evolutionary parlance, it is taboo to actually consider the arguments of these dimwits. The structure of Darwinese, as in 1984, actually inhibits formulating thoughts contrary to Darwinese protocol. Whatever celebrates Darwinian ideas is goodthink; whatever attributes validity to intelligent design is crimethink. The syntax and semantics force thoughts into naturalistic molds – except when Christian terms are borrowed temporarily to get around difficulties (e.g., 07/15/2005)."

The scare quotes, restrictive protocols and good versus bad themes parallel Orwellian thinking depicted in 1984.

"A second requirement is to reinforce the false dichotomy between design/creationist views and “scientific explanation.” The word science must never be used in the same sentence with intelligent design. It is a word reserved strictly for Darwinian materialists, even when the context appeals to mystery, the unknown and the unknowable. Claiming to know the answer is design, and being able to prove it, spoils all the fun of remaining ignorant. He said, “That hour-long lunch helped me appreciate the beauty of the mysterious world we live in.”

"A third requirement in Darwinese is to pretend to be honestly curious and to demean certainty while actually maintaining a dogmatic position. To prove that Shaberman is an accomplished Darwinese speaker, ask him if evolutionary theory itself is up for debate. Imagine what would happen if an interlocutor were to argue that invocations to unknowable Big Bangs and multiverses constitutes a tacit appeal to the supernatural. The Darwinese protocol in such instances is to chant Evolution is science! Creation is religion! as long as necessary to get the interlocutor to leave. News reporters watching on the sidelines will promptly report that the Darwinese speaker achieved a great victory against ignorance and superstition."

Anything that can reinforce supernatural concepts are out of bounds for Darwinists. If multiple universes were a biblical prediction it too would be considered illegitimate.

"A feeling of awe and wonder at things too big to be understood does have its share of euphoria. Mystery can spur one on to seek an explanation. In that sense, it can be a good thing. But mystery is not an end in itself, lest it become a mystery religion. Shaberman just preached a little sermon for the Cult of Lady Luck, one of the denominations of Charlianity. Darwin would be pleased to know that his doctrine of contingency has been extrapolated all the way back into prior worlds of the imagination. This completes his systematic theology: ultimate origins, the present, and ultimate destiny. He is gratified that his completed system produces such warm feelings in the hearts of his disciples. Now that he controls the Ministry of Truth, having ruled all competing ideas out of bounds, he happily pays out his lottery winners in monopoly money. Whatever keeps his devotees hooked enraptured in the realms of eternal ignorance is not too high a price to pay."

Truth is thought of as subjective in western cultures except when objectivity is attached through scientific proclamation. Retaining control of scientific labels signifies power and influence. Many objections to intelligent design could be leveled at beliefs in multi-universes. Since the supernatural is not one of them the multi-universe paradigm remains safe from being ostracized.

Allowing for Change Within a Functional Range

I wrote the following in response to a question concerning specified complexity. The person posing the question indicated that specified complexity (SC) can be generated in an evolutionary context and asked how we would know when it could not be generated. My answer:


The answer lies in analyzing why adaptive changes are possible. They are possible because genomic changes occur within a very narrow range. Too many mutations lead to genomic meltdown and none, or barely none, do not allow for change. This in turn is possible only because key core functions like a functional genome that codes for genomic repair mechanisms, protein and nucleic acid synthesis mechanisms and enzymes required by critical metabolic pathways are already in place. A true test of your hypothesis that evolution produces SC requires testing whether the core enabling functions can evolve. If they must come front loaded then your only move is to become an ID evolutionist.


The raw material for change within a neo-Darwinian paradigm is RM + NS. Random mutations that become fixed in a genome are those that have not been neutralized by genomic repair mechanisms. It is such mechanisms that allow for change within a specified range. The range can also be thought of as that which makes life possible. Outside the range, conditions making change prohibitive also limit adaptive change through mutations and at the other extreme, too many mutations are lethal. A theme of this blog has been that a constricted range was needed at life's origin. If so the complex mechanisms making it possible must have been front loaded. This would be evidence for intelligent design.

The Religion Card

Denyse O'Leary's blog entry entitled Darwinism proponent now simply avoids ID arguments? reveals another tactic utilized to counter intelligent design. Comments of David Rice III about Eugenie Scott are examined. O'Leary describes what seems to be the playing of a religion card which involves disengagement from substantive discussions about intelligent design in favor of talking about religion. The next paragraph quotes Rice:

"Scott used to be (in my opinion) a somewhat respectable foe. But she has not bothered to really engage in the arguments for ID and this radio appearance is one more example of that. The only time the words "intelligent design" leave Scott's mouth is at the 24:48 mark where she said "Actually before I mention intelligent design, I also had a thought regarding that last call...." and then it is never uttered there after - she DIDN"T address intelligent design. This schtick is just not going to work."

And Denyse's comment follows:

"No, it is not going to work. How can it possibly work when major Darwinists spent last year on an "anti-God" campaign? The fact is, Darwinism has always been promoted as the creation story of materialist atheism. No spin aimed at foolish or disaffected clergy is going to change that, nor is Scott going to succeed in characterizing the inevitable blowback from traditional religions and non-materialist philosophies as a form of aggression."

I don't believe it will work either and also notice that it is primarily the Eugenie camp that brings up religion time and time again. She has evidently made up her mind that engaging IDers on scientific matters can backfire and opts for a very unproductive meme instead. Too bad.

Around the Blogosphere 3/18/07

http://telicthoughts.com/new-atheists-a-reaction-to-911/

Mike Gene's interesting thoughts about side effects of 911.


http://telicthoughts.com/evidence-id-and-god/

A blog entry that provoked a great many comments.


http://www.iscid.org/papers/Moody_ConsciousnessComplexity_103103.pdf

An essay about consciousness.


http://mindfulhack.blogspot.com/2007/03/prayer-intercessory-prayer-works.html

Covering a story about research affirming positive effects of prayer.


http://creationevolutiondesign.blogspot.com/2007/03/terrorist-braggart-with-liking-for-sins.html

Are terrorists really motivated by their religious beliefs as claimed? This myth is exposed.


http://www.uncommondescent.com/intelligent-design/the-ncses-behind-the-scenes-role-in-the-sternberg-affair/

Link to the Congressional Report on the Sternberg Affair. Pay attention to the actions of Eugenie Scott.



http://www.newcreationism.org/2007/03/keeping-body-in-sync-stability-of.html

Linking to this article and some information about cellular clocks.


http://www.newcreationism.org/2007/03/stability-of-mrnadna-and-dnadna.html

A blog entry referencing this link.

Taking a Gander at Nanobiology

'Nanobiology Notes' is a blog with some posts worth looking at. The particluar link supplied sends you to a blog entry that contains the following paragraph of interest:

"MIT recently discovered that a protein called MEI-S332 regulates the chromosome cohesion, releasing the chromosomes from each other by adding a phosphate to the binding point. These findings are particularly significant given that researchers have found that levels of MEI-S332 are higher than normal in 90% of all breast cancers. According to Clarke, this might mean that when there’s too much of the protein, the chromosomes don’t separate properly, or it might mean that the MEI-S332 gene is mutated on the chromosomes."

Of course there is more to be learned about this finding but it suggests the possibility of a general cause and effect scenario. At times a mutation adversely affecting one protein will have a cascade effect that eventually results in cancer. In this particular case the culprit might be a regulatory protein that influences the expression of MEI-S332 but that is only a fleeting thought. Things like this resemble whodunnit stories on a molecular level.

Transitional Genomes

Imagine an initial genome that was entirely RNA based i.e. an RNA world scenario. Ignore for the moment some problematic issues it entails but instead focus on the transition to a DNA based genome. Ignore too some legitimate but distracting side issues in order to consider on the following questions. Did that initial transition genome come replete with genes enabling the translation of helicases, DNA and RNA polymerases, topoisomerases and SSB proteins? More generally did that inital DNA genome, that putatively came via the RNA route, have a full complement of function enabling genes? What is the scientific basis for believing blind forces of nature generated this circumstance?

Crossing the Nuclear Pore Complex

'How proteins cross the Nuclear Pore Complex', a post from one of my favorite blogs, states the following in the first paragraph:

"Over this past summer I saw Dirk Görlich give a talk about how the multitude of FG repeats found within the nuclear pore complex (NPC), form a gel like matrix. This "elastic hydrogel" acts as the major barrier within the NPC. Although the gel can prevent the passage of most large molecules (>30kD), it is permeable to nuclear transport receptors (NTRs). Note that all this "story" was published in the November 3rd edition of Science Magazine (link). In that paper there's a nice diagram in the that explains it all:"

FG repeats are nucleoporin repeats that are rich in the amino acids phenylalanine and glycine. The many good diagrams are a staple of the referenced blog.

Protein Modification

An article titled 'Palmitoylation: policing protein stability and traffic' which appreared in Nature Reviews Molecular Cell Biology 8, 74-84 (January 2007). A small snippet from it with links that were added by me:

Palmitate modifies both peripheral and integral membrane proteins and its addition can be permanent or transient, which makes it unique among the lipid modifications of proteins. The presence of palmitate on a protein affects how the protein interacts with lipids and proteins in a membrane compartment, and the reversibility of palmitoylation allows different modes of trafficking between membrane compartments.

The mechanisms involved confer much functional versatility. It is important to remember just how intricate biological functions involving lipids can be when pondering attempts to link evidence of natural lipid formations to a primitive pre-celluar membrane in OOL scenarios. I know the refrain that the present level of biological complexity did not exist in early stages of precellular forms but also would note that viable pre-cellular entities are largely unsupported by data.

Animal Photos

http://www.babyanimalz.com/images/rottie.jpg

http://www.babyanimalz.com/images/babysnowleopard.jpg

My daughter e-mailed me these:

http://news.yahoo.com/photo/070228/481/jak10502280951

http://news.yahoo.com/photo/070228/481/jak11002281031

The Rational Nature of a Belief in a Designer

The following was written recently by an anti-IDist during an exchange in an internet discussion group:

"If we can say nothing substantive about a notion, because we cannot do actual experimentation in the real (i.e. gather data, take measurements. ..) world, then that notion cannot be said to be part of our scientific understanding."

and then shortly thereafter he wrote:

"Which gods, fairies, godmen, goddesses, or intelligent designers can we say have passed any of these requirements?"

This illustrates a common ploy by anti-IDists. The wording varies and at times includes references to ancient Greek gods but the message is the same. In an attempt to ridicule both a viewpoint and the one holding the viewpoint, the anti-IDist will introduce an element of absurdity to infer that an ID position is irrational and contrary to good science. Accordingly there could be no intelligent design because imputing ID could imply a deity and a deity was akin to fantasies like fairies.

The first sentence is another textbook ploy inferring the necessity of "supernatural experiments" when what IDers argue for are positions entailing the testing of natural phenomenon.

At Telic Thoughts Steve Petermann authored the blog entry 'Religion Irrational? Ask a Preeminant Logician', which documents the rational nature of philosophical inferences about God. Specifically referenced was the great mathematician and logician Kurt Godel who is noted, among other things, for his ontological proof. This is the logical formalization of an argument for the existence of God; specifically Saint Anselm's ontological argument.

Of course many others, both before and after Godel, have made rational arguments inferring the existence of God as well. Alvin Plantinga, who has written 'God and others minds. A study of the rational justification of belief in God' is another eminently rational and logical thinker.

Even a brief acquaintance with papers and books addressing the existence of God is enough to show the juvenile nature of the fairies tactic as contrasted with the classics of some of this culture's most brilliant minds.

The Effects of a Change in One Protein

The website 'Medical News Today' published an article titled 'Why some DNA repair fails - Mayo Clinic research' which covers a topic of interest within this blog. Quoting a section of the article:

"From bacteria to humans, cells have evolved sophisticated means of repairing DNA that gets damaged -- by a variety of causes -- ranging from environmental stresses to inherent copying errors. Repair is necessary to prevent accumulations of mutations that can cause disease. Repair is therefore a normal part of a day in the life of DNA. As cells grow and divide, mismatch repair pathways are responsible for identifying irregular growth patterns and repairing specific irregularities in DNA.

Wrong Place at the Wrong Time

Dr. McMurray's group studied a specific mismatch repair protein Msh2-Msh3 and found a paradox: Instead of helping repair DNA damage, under certain conditions, Msh2-Msh3 was actually harming the cell. Msh2-Msh3 did this when it arrived at the wrong place at the wrong time and bound to a specific portion of DNA (CAG-hairpin). This accident of binding at the CAG-hairpin altered the biochemical activity of Msh2-Msh3. This change in biochemical activity, in turn, promoted DNA expansion -- rather than repair -- and changed the function of Msh2-Msh3 from friend of DNA to foe by allowing damaged DNA to go unrepaired. Without DNA repair, mutations accumulate that lead to disease."

This illustrates a general principle common to life. Where a mechanism exists, having a specified function, a malfunction of that mechanism leads to an aberrancy which can induce diseases that are lethal to organisms or compromise their reproductive fitness. In this case the malfunction involves a specific protein whose altered behavoir changed its role from one of DNA repair to DNA expansion. A resulting increase in accumulating mutations can lead to disease.

Around the Blogosphere 3/8/07

http://fluorescentflicker.wordpress.com/2007/02/18/207/

The media and the message at God3's Blog


http://post-darwinist.blogspot.com/2007/03/response-to-student-darwinian.html

Denyse's post addressing a materialist mindset and more.


http://telicthoughts.com/the-protein-world/

The Protein World by Mike Gene


http://www.uncommondescent.com/humor/theory-of-evolution-as-well-tested-as/

Dave Scot:

"We often hear biologists claim the theory of evolution is as well tested as the theory of gravity.

What we don’t often hear is physicists claim the theory of gravity is as well tested as the theory of evolution."


http://www.uncommondescent.com/biology/has-darwinism-contributed-less-to-science-than-alchemy/

Has Darwinism Contributed Less to Science than Alchemy? by Gil Dodgen



http://fluorescentflicker.wordpress.com/2007/03/02/from-goedel-by-way-of-berlinski/

From Goedel by way of Berlinski at God3's Blog



http://www.newcreationism.org/2007/03/simpler-origin-for-life.html

A Simpler Origin for Life


http://telicthoughts.com/templeton-tries-to-set-the-record-straight/

Krauze on setting the record straight at Telic Thoughts

Confirmation Bias on Display

'The Evolution of Religion' is an example of why Darwinism is not science. This paragraph from the linked article will suffice. The remainder is intellectual masterbation. The pargraph:

"As a follow-up of sorts to my genetics of altruism article, The New York Times Magazine had a fascinating, thought-provoking piece on the evolutionary advantages of belief. Scientists have been studying religion from an evolutionary perspective, trying to figure out why religion is universal when it is seemingly maladaptive to survival. Usually, believing in nonexistent things and expending energy on nonproductive pursuits will make it harder to survive, not easier."

The first clue that investigators are off track is the observation that something is "seemingly maladaptive to survival." Of course, considering an appearance as being actually what it seems to be is unthinkable when the observation runs counter to standard evolutionary paradigms. When mainstreamers run into this type of roadblock imaginations go into gear and confirmation bias replaces objectivity.

The second indicator of poor science is the unscientific metaphysical basis to the conclusion. A belief that God is non-existent previously had been wisely consigned to non-scientific atheist or religious debate forums. Incorporation of this belief into mainstream scientific investigations is most unfortunate in that it a) assumes a scientifically undemonstrable premise and b) does so to further some unscientific metaphysical objectives on the part of enthusiasts for such studies. The assumption of God as an illusion could be worked into a tentative premise as long as those utilizing the premise were able to specify both how it would be falsifed and how its opposite assumption could be validated. Even then there would be a need to show how all this is essential to the derivation of a testable hypothesis.

Stephen Jay Gould's "Non-Overlapping Magisterium" was not without its problems but it did have value in illustrating the utility of boundaries for both religious and scientific claims. If science is based on natural methodology then how is it able to assess supernatural claims? One is entitled to disbelieve supernatural claims but if the disbelief is said to be empirically grounded then where is the beef? A proclivity to assume an illusory nature to religion and base scientific claims on this threatens to the integrity of science.

Hard Wired?

Joy and Mike Gene have both recently posted blog entries ("Hard-Wired" for God: Part 2 and Some Thoughts on "Darwin's God") related to religion, God and evolution. Joy's post references the article Are Humans "Hard Wired" for God? From that article:

"Atran's research interests have led him to the question of God, which he approaches from cognitive science and evolutionary biology. He asks why religion has persisted for so long if it provides no evolutionary benefits. His answers reveal a deep divide within evolutionary science - the debate between those who believe that belief in God originally served some evolutionary, adaptive function and those who believe that belief in God is merely a byproduct or consequence of some other adaptation in the evolution of the human brain."

Philipp Johnson's recently published article, Intelligent Design in Biology: the Current Situation and Future Prospects, contains some remarks that bring up unasked questions. Quoting Johnson:

"But religious questions may be reasonable and important questions. Here is an example: I’ve repeatedly posed the question, “Is God real, or imaginary?”. Evolutionary naturalism classes god among the subjective products of the human brain, and thus among the products of evolution itself. If God is truly real, however, and really our creator, then to enforce a definition of knowledge based upon the assumption that ONLY nature is real, and that God exists only in the human imagination, would be to make a big mistake."

If God is not the construct of human imagination, but has an independent existence, then analyses based on the imagination assumption need to be revisited. Anyone who spends much time discussing evolution and intelligent design on internet forums, will encounter the argument that science cannot make intelligible claims about the supernatural, as its methodology is limited to the natural world. The properties attributed to God do not allow a scientific declaration as to his existence or non-existence. The question lies outside the boundary of science.

Yet an assumption of God's non-existence is inherent to evolutionary explanations that cite selection of a hard-wired mental property as linked to illusory adaptive beliefs. This raises a question or two. Are related musings about what mental faculties might be hard-wired, prejudiced by a non-scientific determination of God's existence, which makes an illusory assumption inevitable? To revise the question, would the assumption that God's existence is real negate hard-wired findings or simply attribute them to design? If this last assumption about God is deemed non-scientific (as opposed to unscientific) then how can findings based on the negation of a belief, presumed to lie outside the purview of science, be deemed scientifically plausible? Mike Gene's blog entry had this to say:

"I would also add that the truth of God’s existence is not dependent on humans having some supernatural ability to perceive such existence." Indeed.

More from Johnson:

"The goal of the Intelligent Design Movement is to achieve an open philosophy of science that permits consideration of any explanations toward which the evidence may be pointing. This is different from the current restrictive philosophy that rules out of consideration the possibility that a creator may be responsible for our existence, even if the evidence is pointing in that general direction."

This leads to another set of questions. How are hard-wired hypotheses tested? Can they be tested by allowing for the hypothesis that God is not illusory? What type of test results would advance a design paradigm and which would oppose it? Or are inferences limited by the artificial scope of the inquiry?

White and Dark Meat

I came across a blog Omics! Omics! today and read a blog entry containing this interesting tidbit.

"First though, we need to review some biochemistry. The metabolism of sugar to energy in our cells requires a complex pathway of events. The system can be divided into three basic subsystems: glycolysis, the citric acid (or Krebs) cycle, and the respiratory electron transport chain. The handoff from glycolysis to the citric acid cycle is the molecule pyruvate. However, this three stage system requires oxygen; in the absence of oxygen energy production halts at glycolysis. Which means the cell needs to deal with all that pyruvate, or the system stalls.

The first biotechnologists discovered that yeast has a very interesting solution to this problem: it converts the pyruvate to ethanol. But in animals, the endpoint is instead lactic acid. It is lactic acid buildup that gives you a burning sensation from tired muscles. Obtaining energy solely from glycolysis is far less effective than going the whole scheme (about 6X if I remember correctly), so animals tend to reserve it for special occasions -- such as quick bursts of muscle activity or other occasions when oxygen can't get to the cells fast enough. As my freshman bio prof pointed out, this leads to the white meat vs. dark meat dichotomy of chickens: chickens walk all the time, so the legs operate in the aerobic regime, whereas the wings are for short flights and operate anerobically. The oxygen storage protein myoglobin contains oxygen & gives the dark meat its characteristic color."

It works for turkeys too; a favorite of mine. BTW, oxygen can be toxic to organisms lacking enzymes that prevent destructive effects this element can engender. Aerobic glycolysis requires oxygen and anaerobic glycolysis can occur without it. Pyruvate is the end product of aerobic glycolysis. Pyruvate is then converted in another pathway- the tricarboxylic acid cycle.

H4 Involvement in DNA Repair

A news article 'Mayo Clinic Uncovers Key Step in Repair Mechanism of DNA Double-Strand Breaks' reports of a discovery related to repairing DNA double-strand breaks. Research results were published in 'Cell' (subscription required).

From the first linked site:

"It was known from previous studies in fission yeast that histone H4 and Crb2 (the protein counterpart of 53BP1 in fission yeast) are important components of the DNA repair machinery. "Our work shows that this also is true in humans and that direct binding of 53BP1 to histone H4 is necessary to bring 53BP1 near the damaged DNA. In a similar fashion, we also demonstrated that Crb2 directly interacts with histone H4," says Mayo Clinic structural biologist Georges Mer, Ph.D., who led the study."

A major theme of this blog is emphasizing the importance of DNA repair mechanisms. Not only are they critical to life, they are critical in determining the plausibility of competing theories as to life's orgin and development. The cited study confirmed what researchers suspected based on previously established data obtained from the study of fission yeast. Interactions with histone H4 in humans are needed to allow protein 53BP1 to get near damaged DNA. DNA repair is like a book with many chapters. Histone H4 merits a chapter of its own.

Exposing a Common Fallacy

Some very good information and analytical insight is found in the comment section of posts made at Telic Thoughts. A frequent complaint leveled at ID is that it is nothing more than a Trojan Horse for religious doctrine, particularly that of Christianity. A commenter known as Analyysi referred to the book 'Living with Darwin: Evolution, Design and the Future of Faith' which is authored by Philip Kitcher. Analyysi referred to this quote noting a logical point ot two.


"Advertising intelligent design as independent of religious doctrine is accurate in one important sense. To claim that some kind of organisms are products of intelligent design does not logically entail any conclusion about the existence of a deity, let alone any specific articles on Christian faith." (p. 6)

"Although there are grounds for suspicion, I shall treat intelligent design as its leaders characterize it, as a hypothesis put forward to identify and account for certain natural phenomena. The sociological fact that the hypothesis is welcomed by a significant number of Christians, and by some religious people of other faiths, does not make it an intrisically religious doctrine. A proposal about natural world need have no specifically religious content to be more combatible with particular religious ideas than its equally naturalistic rivals." (p. 7)

Source:
Philip Kitcher, Living with Darwin:
Evolution, Design and the Future of Faith
(Oxford University Press, 2007)

Well said Philip Kitcher. An excellent rebuttal to a common misconception.

Objections to Rational Thought

The blogsite 'Reasoning Repaired' features a blog entry titled Random Thoughts from my Journal which contains some comments I've included in this post. It is obvious to anyone who has spent a significant amount of time engaged in discussions about intelligent design, that its opponents are often driven by motives totally unrelated to scientific data. A primary source of opposition springs from feelings about God; usually God as depicted (or thought to be depicted) biblically. Some specific complaints relate to evil and recent comments at Telic Thoughts demonstrate this. From 'Random Thoughts from my Journal':

● "If the atheist demands a “scientific” answer to the question, “if God is all good and all powerful, why is there evil in the world?” Well, first of all, evil is not a “thing” but a privation—a certain lack of good. Second, maybe they should ask themselves “if there is no God, then why is there so much good in the world?” Unless, of course, one is an intellectual pee-wee like Richard Dawkins who simply argues there are no such things as good and evil… and yet he rails against God as being “evil.” It is not so much that we need a rational explanation of God, as we need a psychological explanation of atheists."

The lack of good can be reduced to an absence of love. How is love defined?

1 Corinthians 13 (New American Standard Bible)

4Love is patient, love is kind and is not jealous; love does not brag and is not arrogant,

5does not act unbecomingly; it does not seek its own, is not provoked, does not take into account a wrong suffered,

6does not rejoice in unrighteousness, but rejoices with the truth;

7bears all things, believes all things, hopes all things, endures all things.

8Love never fails; but if there are gifts of prophecy, they will be done away; if there are tongues, they will cease; if there is knowledge, it will be done away.

Where one posseses and practices the foregoing evil does not appear. When these qualities are absent evil is inevitable. Evil is connected with individuals who have a capacity to choose. The presence or absence of evil can be traced to the condition of individual human hearts. Attributing evil to the creator of those exercising free will is to condemn individuality itself. It is a demand for programmed robots in place of humanity. More from the linked blog:


● Philosophy doesn’t appeal to faith or to religion to understand the world—it cannot, in fact, do so for it would lose its autonomy. But philosophy can demonstrate the existence of a First Cause and of a Designer of the world (not in the Intelligent Design movement’s sense).

A first cause is the product of rational thinking. It stands in opposition to the model of an infinite chain of causes and effects. Thus a belief in God also is rational and not the product of superstition, as atheists would have us believe.

The Physics of Signaling

The Science Sampler blog features a post on cellular signaling. From the opening paragraph:

"This is a very simple paper that attempts to answer a simple question – does physics play any role in regulating cell siganling. As cell biologists we generally like to think of signaling cascades as regulating cellular processes. We consider that an extracellular ligand binds a receptor triggering a cascade that results in some cellular behavior. The Odde lab however takes a different approach and proposes that physics, specifically cell size and shape play an important role in regulating cell signaling."

The issues raised by the Odde lab are far from settled and as the blog author pointed out it raised a chicken- egg scenario that is not uncommon in biology. The question raised was whether physics led to signaling or did signaling come first? They are consistent with each other but which is the actual causal factor accounting for the other?